1. Analysis of Genomic Characteristics of SARS-CoV-2 in Italy, 29 January to 27 March 2020
- Author
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Alessandra Lo Presti, Angela Di Martino, Giovanni Faggioni, Francesco Giordani, Silvia Fillo, Anna Anselmo, Vanessa Vera Fain, Antonella Fortunato, Giancarlo Petralito, Filippo Molinari, Stefano Palomba, Riccardo De Santis, Stefano Fiore, Concetta Fabiani, Giuseppina Di Mario, Marzia Facchini, Laura Calzoletti, Florigio Lista, Giovanni Rezza, and Paola Stefanelli
- Subjects
SARS-CoV-2 evolution ,genomics ,gene flows ,dated phylogeny ,Microbiology ,QR1-502 - Abstract
We performed next-generation sequencing (NGS), phylogenetic analysis, gene flows, and N- and O-glycosylation prediction on SARS-CoV-2 genomes collected from lab-confirmed cases from different Italian regions. To this end, a total of 111 SARS-CoV-2 genomes collected in Italy between 29 January and 27 March 2020 were investigated. The majority of the genomes belonged to lineage B.1, with some descendant lineages. The gene flow analysis showed that the spread occurred mainly from the north to the center and to the south of Italy, as confirmed by epidemiological data. The mean evolutionary rate estimated here was 8.731 × 10−4 (95% highest posterior density, HPD intervals 5.809 × 10−4 to 1.19 × 10−3), in line with values reported by other authors. The dated phylogeny suggested that SARS-CoV-2 lineage B.1 probably entered Italy between the end of January and early February 2020. Continuous molecular surveillance is needed to trace virus circulation and evolution.
- Published
- 2022
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